Parameters Input values
Folder name : Example data
Sequence name : CDH1
Reference genome : BSgenome.Hsapiens.UCSC.hg19
Type of experiment : Direct-BSP
Group order : LowmethylatedDNA, HighmethylatedDNA
Date of analysis : 2022-05-03 14:40 
## Joining, by = c("CG_nb", "chromosome", "start", "end")
## Joining, by = c("CG_nb", "chromosome", "start", "end")
## Joining, by = c("CG_nb", "chromosome", "start", "end")
## Joining, by = c("CG_nb", "chromosome", "start", "end")
## Joining, by = c("CG_nb", "chromosome", "start", "end")
## Joining, by = c("CG_nb", "chromosome", "start", "end")
## Joining, by = c("CG_nb", "chromosome", "start", "end")
## Joining, by = c("CG_nb", "chromosome", "start", "end")
## Joining, by = c("CG_nb", "chromosome", "start", "end")
## Joining, by = c("CG_nb", "chromosome", "start", "end")
## Joining, by = c("CG_nb", "chromosome", "start", "end")

Files content

Data files content

Parameters Data files content
Sequence name : CDH1
Collections :
Groups : LowmethylatedDNA, HighmethylatedDNA, High methylated DNA, Low methylated DNA
Replicates : 1, 2, 3

Data files paths

File paths used for the analysis

D:/Documents/These/ABSP/results/Example data/CDH1/individual_results_direct/data/CDH1_High methylated DNA_1_methdata.csv
D:/Documents/These/ABSP/results/Example data/CDH1/individual_results_direct/data/CDH1_High methylated DNA_2_methdata.csv
D:/Documents/These/ABSP/results/Example data/CDH1/individual_results_direct/data/CDH1_High methylated DNA_3_methdata.csv
D:/Documents/These/ABSP/results/Example data/CDH1/individual_results_direct/data/CDH1_Low methylated DNA_1_methdata.csv
D:/Documents/These/ABSP/results/Example data/CDH1/individual_results_direct/data/CDH1_Low methylated DNA_2_methdata.csv
D:/Documents/These/ABSP/results/Example data/CDH1/individual_results_direct/data/CDH1_Low methylated DNA_3_methdata.csv

Methylation data

Methylation data of replicates

chr16:68771035-68771036 chr16:68771037-68771038 chr16:68771045-68771046 chr16:68771051-68771052 chr16:68771059-68771060 chr16:68771064-68771065 chr16:68771073-68771074 chr16:68771090-68771091 chr16:68771092-68771093 chr16:68771112-68771113 chr16:68771138-68771139 chr16:68771143-68771144 chr16:68771150-68771151 chr16:68771159-68771160 chr16:68771182-68771183 chr16:68771200-68771201 chr16:68771203-68771204 Mean SD
High methylated DNA 1 81.43 100.00 100 83.35 100.000 95.72 77.22 97.52 100 99.63 100 100.00 100.00 NA NA NA NA 94.99 8.36
High methylated DNA 2 83.50 100.00 100 84.08 100.000 95.84 77.83 98.55 100 99.73 100 100.00 100.00 NA NA NA NA 95.35 7.93
High methylated DNA 3 96.39 100.00 100 76.89 91.865 98.21 74.25 99.56 100 99.90 100 100.00 100.00 99.62 100 100 100 96.28 8.08
Low methylated DNA 1 0.00 0.00 0 0.00 0.000 6.00 0.00 0.00 0 0.00 0 1.69 1.98 NA NA NA NA 0.74 1.72
Low methylated DNA 2 13.16 1.33 0 1.40 0.000 3.40 0.00 0.00 0 0.00 0 23.22 NA NA NA NA NA 3.54 7.24
Low methylated DNA 3 0.00 0.00 0 0.00 0.000 0.00 0.00 0.00 0 0.00 0 0.00 NA NA NA NA NA 0.00 0.00

Methylation data of groups

chr16:68771035-68771036 chr16:68771037-68771038 chr16:68771045-68771046 chr16:68771051-68771052 chr16:68771059-68771060 chr16:68771064-68771065 chr16:68771073-68771074 chr16:68771090-68771091 chr16:68771092-68771093 chr16:68771112-68771113 chr16:68771138-68771139 chr16:68771143-68771144 chr16:68771150-68771151 chr16:68771159-68771160 chr16:68771182-68771183 chr16:68771200-68771201 chr16:68771203-68771204 Mean SD
High methylated DNA 87.11 100.00 100 81.44 97.29 96.59 76.43 98.54 100 99.75 100 100.0 100.00 99.62 100 100 100 96.28 7.30
Low methylated DNA 4.39 0.44 0 0.47 0.00 3.13 0.00 0.00 0 0.00 0 8.3 1.98 NaN NaN NaN NaN 1.44 2.51

Plots of replicates

Lollipop plots

Sample order : as-is

Type : proportional

Type : condensed

Genomic plots

Sample order : as-is

Plots of groups

Lollipop plots

Sample order : as-is

Type : proportional

Type : condensed

Genomic plots

Sample order : as-is

Statistics

Descriptive statistics of groups

Methylation by CpG positions

CpG number CpG coordinate Collection Group N Methylation mean SD SEM Confidence interval of 95% (±)
1 chr16:68771035-68771036 High methylated DNA 3 87.11 8.11 4.68 20.14
1 chr16:68771035-68771036 Low methylated DNA 3 4.39 7.60 4.39 18.87
2 chr16:68771037-68771038 High methylated DNA 3 100.00 0.00 0.00 0.00
2 chr16:68771037-68771038 Low methylated DNA 3 0.44 0.77 0.44 1.91
3 chr16:68771045-68771046 High methylated DNA 3 100.00 0.00 0.00 0.00
3 chr16:68771045-68771046 Low methylated DNA 3 0.00 0.00 0.00 0.00
4 chr16:68771051-68771052 High methylated DNA 3 81.44 3.96 2.28 9.83
4 chr16:68771051-68771052 Low methylated DNA 3 0.47 0.81 0.47 2.01
5 chr16:68771059-68771060 High methylated DNA 3 97.29 4.70 2.71 11.67
5 chr16:68771059-68771060 Low methylated DNA 3 0.00 0.00 0.00 0.00
6 chr16:68771064-68771065 High methylated DNA 3 96.59 1.40 0.81 3.49
6 chr16:68771064-68771065 Low methylated DNA 3 3.13 3.01 1.74 7.47
7 chr16:68771073-68771074 High methylated DNA 3 76.43 1.92 1.11 4.76
7 chr16:68771073-68771074 Low methylated DNA 3 0.00 0.00 0.00 0.00
8 chr16:68771090-68771091 High methylated DNA 3 98.54 1.02 0.59 2.53
8 chr16:68771090-68771091 Low methylated DNA 3 0.00 0.00 0.00 0.00
9 chr16:68771092-68771093 High methylated DNA 3 100.00 0.00 0.00 0.00
9 chr16:68771092-68771093 Low methylated DNA 3 0.00 0.00 0.00 0.00
10 chr16:68771112-68771113 High methylated DNA 3 99.75 0.14 0.08 0.34
10 chr16:68771112-68771113 Low methylated DNA 3 0.00 0.00 0.00 0.00
11 chr16:68771138-68771139 High methylated DNA 3 100.00 0.00 0.00 0.00
11 chr16:68771138-68771139 Low methylated DNA 3 0.00 0.00 0.00 0.00
12 chr16:68771143-68771144 High methylated DNA 3 100.00 0.00 0.00 0.00
12 chr16:68771143-68771144 Low methylated DNA 3 8.30 12.95 7.47 32.16
13 chr16:68771150-68771151 High methylated DNA 3 100.00 0.00 0.00 0.00
13 chr16:68771150-68771151 Low methylated DNA 1 1.98 NA NA NaN
14 chr16:68771159-68771160 High methylated DNA 1 99.62 NA NA NaN
14 chr16:68771159-68771160 Low methylated DNA 0 NaN NA NA NaN
15 chr16:68771182-68771183 High methylated DNA 1 100.00 NA NA NaN
15 chr16:68771182-68771183 Low methylated DNA 0 NaN NA NA NaN
16 chr16:68771200-68771201 High methylated DNA 1 100.00 NA NA NaN
16 chr16:68771200-68771201 Low methylated DNA 0 NaN NA NA NaN
17 chr16:68771203-68771204 High methylated DNA 1 100.00 NA NA NaN
17 chr16:68771203-68771204 Low methylated DNA 0 NaN NA NA NaN

Methylation means of all CpG positions

Collection Group N Methylation mean SD SEM Confidence interval of 95% (±)
High methylated DNA 3 95.54 0.67 0.38 1.65
Low methylated DNA 3 1.43 1.87 1.08 4.64

Student’s T test

For each CpG position

Warning: N < 3 for at least one group at one position, T tests can not be performed.

Error: T tests could not be performed on the provided data.

For means of CpG positions

Student’s T test (two-samples, unpaired)

Collection Compared group 1 Compared group 2 N group 1 N group 2 p-value p-value significance level
High methylated DNA Low methylated DNA 3 3 2.34e-05 ****

Boxplots

For each CpG position

Boxplots represent methylation median and quartiles of each group with errors bars. Methylation mean are represented as diamond shapes.

The p-values and p-value significance levels are determined by Student’s T tests (unpaired).

Warning: N < 3 for at least one group at one position, T tests can not be performed.

p-values

p-values significance levels

For means of CpG positions

Boxplots represent methylation median and quartiles of each group with errors bars. Methylation mean are represented as diamond shapes.

The p-values and p-value significance levels are determined by Student’s T tests (unpaired).

p-values

p-values significance levels

Methylation profile plots

Each points represent the methylation mean of clones or replicates for a given CpG site.
The p-values and p-value significance levels are determined by Kruskal-Wallis tests.

Type : proportional

p-values

## Warning: Removed 4 row(s) containing missing values (geom_path).
## Warning: Removed 4 rows containing missing values (geom_point).

p-values significance levels

## Warning: Removed 4 row(s) containing missing values (geom_path).
## Removed 4 rows containing missing values (geom_point).

Type : condensed

p-values

## Warning: Removed 4 row(s) containing missing values (geom_path).
## Removed 4 rows containing missing values (geom_point).

p-values significance levels

## Warning: Removed 4 row(s) containing missing values (geom_path).
## Removed 4 rows containing missing values (geom_point).

Output data

Directories